1. Welcome to BIO 94!
TA: Jen
Office hours:
Friday, 2:00-3:00, BS3 2130

2. Tree-thinking Quiz BIO94 W16 Answers included
Quiz based on “The Tree-Thinking Challenge”, David A. Baum,* Stacey DeWitt Smith, Samuel S. Donovan, Science 310, 979 (2005)

3. First, some terminology . . .

4. Terms associated with phylogenetic trees
Tips represent terminal taxa (or genes) of a lineage, usually extant
(a.k.a. leaf, or terminal node or just a terminal) A B C D E
A, B, C, D, E: can be a strain, a population, a species, etc. Anything that forms a closely-related unit.
A clade is a group of taxa that includes a common ancestor and ALL of its descendants. These are nested within one another.
Like reading a family tree
The ancestor of all of the descendents (such as extant species or groups) is at the bottom.
As you move towards the tips, you move forward in time

5. Terms associated with phylogenetic trees
Nodes represent branching or splitting points on a tree; may represent extinct or hypothetical ancestor(s) A B C D E
1. Each node on a tree is an ancestor. The branches descending from each ancestor (in the direction away from the root) lead to its descendants.
2. Each ancestral node can be rotated. This places the descendants on different parts of the printed page, but does not change their relationships to one another.
3. All descendants of a particular ancestor are more closely related to one another than they are to any other taxa on the tree, no matter where they happen to be placed on the printed page.
What has happened where the lines split?
Speciation! These are the nodes, and they represent common ancestors.
Which is the common ancestor of A and B? Of B and C? Of D and A?

6. Terms associated with phylogenetic treesB C D E
“Root” refers to the node at the ‘base’ of the tree; represents the common ancestor of all descendant taxa in the tree.
Time
Note: some trees have no ‘root’, to be discussed later

7. Terms associated with phylogenetic trees
Branches are the parts of a tree that connect the node or the nodes to the tips (aka internodes, edges) A B C D E a c b
Note: branches such as a, b, and c are sometimes referred to as ‘internal branches’

8. Terms associated with phylogenetic treesB C D E
Topology of a tree refers to the overall pattern of connectedness of the nodes and termimal taxa
The pattern of branching (i.e., the topology) is what matters here. Branch lengths are irrelevant--they are simply drawn in whatever way makes the tree look most tidy. (Unless it’s a phylogram, where branch lengths are meaningful and usually indicate the estimated length of time since divergence.)

9. Tree equivalence:
Format doesn’t matter, but attachment points do.
Pay attention to the branching pattern and nestedness (what stacks within what).
4. Trees can be printed in a variety of formats (rectangular, circular, etc.) and they can be placed on the page in a variety of ways as well (root at the bottom of the page, or on the left, etc.). None of this changes the relationships of the taxa shown.
The basic rule is that if you can change one tree into another tree simply by twisting, rotating, or bending branches, without having to cut and reattach branches, then the two trees have the same topology and therefore depict the same evolutionary history.
None of this changes the relationships of the taxa shown.

10. Format doesn’t matter, but attachment points do.
Tree equivalence:
Tree equivalence:
Format doesn’t matter, but attachment points do.
Pay attention to the branching pattern and nestedness (what stacks within what).
Warm up question.
These trees show the same information. The inner group is just rotated around a node.

11. Consider the following evolutionary tree or phylogeny . . .
green algae
fungus
moss
fern
conifer x y
This is the start of the quiz proper.
Take out a pencil and a blank piece of paper. b
Referring to the tree above, which is an accurate statement of relationships?
a) a moss is more closely related to a green alga than to a fern
b) a moss is more closely related to a fern than to a green alga
c) a moss is equally related to a green alga and a fern
d) a moss is related to a green alga but is not related to a fern

12. Consider another example . . .
fish
lizard
crocodile
dinosaur
bird x y b
2a. Referring to the tree above, which is an accurate statement of relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird

13. Does this help?
Still b
2b. Referring to the tree above, which is an accurate statement of relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird

14. And another example . . .
gibbon
orangutan
gorilla
chimp
human x c
3. Referring to the tree above, which is an accurate statement of relationships?
a) a gibbon is more closely related to a orangutan than to a human
b) a gibbon is more closely related to a human than to a orangutan
c) a gibbon is equally related to a human and a orangutan
d) a gibbon is related to a orangutan but is not related to a human

15. How about this one ?
sunflower
fern
fungus
termite
mouse a d c b e
4. Which of the five nodes marked on the tree above corresponds to the common ancestor(s) of a mouse and a fungus?
5. Which of the five nodes marked on the tree above corresponds to the most recent common ancestor of a mouse and a fungus?
4. Cde
5. Just c

16. e) hornworts, mosses, etc.
secondary xylem (wood)
hornworts, mosses, etc.
Lepidodendron
ferns
seeds
Equisetum
true leaves
loss of leaves
tree habit
gymnosperms
angiosperms
common ancestor x
6. In the above example, assume the common ancestor of these plants was a herb (herbaceous, i.e., not woody) and did not produce true leaves or seeds. Based on the phylogeny and assuming that all evolutionary changes in these traits are shown, which of the tips has a tree habit but lacks true leaves?
a) angiosperms
b) ferns
c) Equisetum
d) Lepidodendron
e) hornworts, mosses, etc.
D, Lepidodendron
Blue tick marks identify lineages along which indicated trait changes have occurred

17. Consider the following evolutionary tree or phylogeny . . .
green algae
fungus
moss
fern
conifer
“b” is correct. The most recent common ancestor of moss & a fern, node x, is more recent in time (compared to present) than the most recent common ancestor of a moss & a green alga, node y. x y
Referring to the tree above, which is an accurate statement of relationships?
a) a moss is more closely related to a green alga than to a fern
b) a moss is more closely related to a fern than to a green alga
c) a moss is equally related to a green alga and a fern
d) a moss is related to a green alga but is not related to a fern

18. Consider another example . . .
fish
lizard
crocodile
dinosaur
bird
Again, “b” is correct. The most recent common ancestor of a crocodile & a bird, node x, is more recent in time (compared to present) than the most recent common ancestor of a croc & a lizard, node y. x y
2a. Referring to the tree above, which is an accurate statement of relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird

19. Does this help?
No, not really. “b” is the correct answer. While a crocodile may appear more “similar” to a lizard in anatomy, morphology, ecology, etc., the crocodile is more closely related to a bird than to a lizard based on recency of common ancestry.
2b. Referring to the tree above, which is an accurate statement of relationships?
a) a crocodile is more closely related to a lizard than to a bird
b) a crocodile is more closely related to a bird than to a lizard
c) a crocodile is equally related to a bird and a fish
d) a crocodile is related to a lizard but is not related to a bird

20. And another example . . .
gibbon
orangutan
gorilla
chimp
human
“c” is correct. Because the gibbon shares the same most recent common ancestor with both an orangutan and a human (node x), the gibbon is “equally” related to both x
3. Referring to the tree above, which is an accurate statement of relationships?
a) a gibbon is more closely related to a orangutan than to a human
b) a gibbon is more closely related to a human than to a orangutan
c) a gibbon is equally related to a human and a orangutan
d) a gibbon is related to a orangutan but is not related to a human

21. How about this one ?
sunflower
fern
fungus
termite
mouse a d c b e
Nodes “c”, “d”, and “e” are common ancestors of the mouse and fungus.
Node “c” is the most recent common ancestor of the mouse and fungus.
4. Which of the five nodes marked on the tree above corresponds to the common ancestor(s) of a mouse and a fungus?
5. Which of the five nodes marked on the tree above corresponds to the most recent common ancestor of a mouse and a fungus?

22. e) hornworts, mosses, etc.
secondary xylem (wood)
hornworts, mosses, etc.
Lepidodendron
ferns
seeds
Equisetum
true leaves
loss of leaves
tree habit
gymnosperms
angiosperms
common ancestor
“d”, Lepidodendron. The change from herbaceous to tree habit occurred along the branch leading to this tip taxon, while the change from no leaves to true leaves occurred after Lepidodendron branched off from the rest of the tip taxa. x
6. In the above example, assume the common ancestor of these plants was a herb (herbaceous, i.e., not woody) and did not produce true leaves or seeds. Based on the phylogeny and assuming that all evolutionary changes in these traits are shown, which of the tips has a tree habit but lacks true leaves?
a) angiosperms
b) ferns
c) Equisetum
d) Lepidodendron
e) hornworts, mosses, etc.
Blue tick marks identify lineages along which indicated trait changes have occurred

23. Who’s more related to whom?

24. How to determine who’s related to whom? Shared derived traits.

25. How do we figure out the evolutionary relationships among organisms?
We rely on shared, derived characters
Shared = shared, found in multiple related groups/species
Derived = new, non-ancestral
Characters = heritable traits of an organism (e.g., morphology, physiology, biochemistry, behavior, developmental pattern, chromosome features, gene sequences, etc.)
So, groups of organisms that share more of these characters by common ancestry are likely to be more closely related

26. Homology, Analogy, and Cladistics
Homologies are characteristics that are alike because of common descent
Analogies, or homoplasies, are characteristics that are alike in form or function (probably due to similar selective pressures), but do not share a common ancestry (evolved independently). This is known as convergence.
Give your favorite example to illustrate convergence. Succulents in multiple continents, gliding rodents, whatever.

27. Insect wing and bird wing = convergence
Insect wing and bird wing = convergence. Same function, different origin.
Bat arm and bird arm and human arm (bones) = homology.
But the fact that birds and bats both fly is convergence.

28. Cladistics
A cladogram is a graphical representation of the relatedness of species (their phylogeny) based on the number of characteristics from common ancestors that they share (can be morphology, behavior, genes, etc.)
One axis is time, with the top (or right) being the present and the bottom (or left) being earlier.
Nodes are the splitting points. Represent the most recent common ancestor of two or more taxa.
The more homologies, the more closely related.

29. Parsimony
Parsimony – the fewest number of evolutionary changes is the most likely explanation. For example, you don’t want to have feathers evolve 317 times in your phylogeny if you can help it. The idea that feathers evolved only once is more parsimonious.
However, if you have a whole bunch of traits on which to base your cladogram, it might be simpler for one trait to evolve independently multiple times. This trait is an analogy.

30. Monophyletic group
A proper clade. Includes a common ancestor and ALL descendants. A B C D E F

31. Paraphyletic Group
Includes a common ancestor and only SOME descendants. (e.g. great apes – doesn’t include humans, others?) A B C D E F

32. Polyphyletic Group
A group that share a common trait, but the trait is an analogy (which means?) e.g., birds of prey, marine mammals, others? A B C D E F
Warm bloodedness has evolved multiple times

33. Comparison Monophyletic = upper left Paraphyletic = upper right
Polyphyletic = bottom

34. Clarification
Ancestral/derived are terms that have to be used relatively.
For example, when comparing reptiles, dinosaurs, birds, and mammals, body hair is a derived feature for mammals. However, when discussing mice, rats, dogs, and people, body hair is ancestral (the most recent common ancestor of all four groups had body hair).

35. Evolution is… What causes this to happen?
A change in gene frequencies in a population of organisms over time.
Anyone remember?
What causes this to happen?

36. Mechanisms of Evolution
Mutations
Random changes in genetic material – generates variation in a population
Natural Selection
Process by which those more adapted to survive pass on more genes
Sexual Selection
Really a kind of natural selection. Process by which those more adapted to successfully mate pass on more genes
Gene flow
Transfer of genes between 2 populations
Genetic Drift (Founder Effect, Bottlenecking) – evolution caused by random events, like a new geographic separation or event that randomly kills individuals.

37. Natural Selection Natural selection requirement= Heritability
Natural selection requirement= Variation
Natural selection requirement= Reproductive Consequences

38. How do these small changes in gene frequencies explain all the species on earth today?
It’s been a long time
The Earth is ~4.5 BILLION yrs old
540 MILLION yrs ago – 1st vertebrates
150 million years later, 1st vertebrates on land
200 million years later, 1st vertebrates in the air!
Can replace images

39. Why do some organisms/ structures seem perfect?
It has taken a long time, and many, many generations.
Look closer – there are a lot of imperfections.
Vestigial organs
Imperfect “design”
The environment is always changing.
Variation must be present for selection to act upon.